edu.mssm.crover.util
Class AlignmentReader

java.lang.Object
  |
  +--edu.mssm.crover.util.AlignmentReader

public class AlignmentReader

extends java.lang.Object

Class to read the sequences in a two-sequence alignment, and then find pairs of residues that are conserved or switched between them.

Author:

luce

Constructor Summary

AlignmentReader()

Method Summary

java.util.Hashtable	fillConservedResidues()
java.util.Collection	getSequences()
static void	main(java.lang.String[] args)
void	printConservedResidues(java.io.File f, boolean all)
void	readAlignment(java.io.File f)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignmentReader

public AlignmentReader()

Method Detail

readAlignment

public void readAlignment(java.io.File f)
                   throws java.io.IOException

java.io.IOException

getSequences

public java.util.Collection getSequences()

fillConservedResidues

public java.util.Hashtable fillConservedResidues()

printConservedResidues

public void printConservedResidues(java.io.File f,
                                   boolean all)
                            throws java.io.IOException

java.io.IOException

main

public static void main(java.lang.String[] args)